Table 5

SSRs in 454 ESTs.

Type of SSR repeat

Reference based assembly

De novo assembly of remaining reads

Total


Di

1,267 (54)

10,366 (1,487)

11,633 (1,541)

Tri

551 (520)

2,480 (1,748)

3,031 (2,268)

Tetra

23 (19)

397 (192)

420 (211)


Total

1,841 (593)

13,243 (3,427)

15,084 (4,020)


Numbers of di-, tri-, and tetranucleotide simple sequence repeats (SSRs) occurring in contigs from both the reference-based and de novo assemblies. In parentheses following the number of loci identified are the number of potentially amplifiable loci for which PCR primers were designed in BatchPrimer3 [42] with stringent criteria (see Additional file 1: Supplemental Table S1).

Parchman et al. BMC Genomics 2010 11:180   doi:10.1186/1471-2164-11-180

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